Job ID = 14170138 SRX = SRX8556381 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19678016 spots for SRR12024937/SRR12024937.sra Written 19678016 spots for SRR12024937/SRR12024937.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170721 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:23:39 19678016 reads; of these: 19678016 (100.00%) were paired; of these: 16121958 (81.93%) aligned concordantly 0 times 2714790 (13.80%) aligned concordantly exactly 1 time 841268 (4.28%) aligned concordantly >1 times ---- 16121958 pairs aligned concordantly 0 times; of these: 643882 (3.99%) aligned discordantly 1 time ---- 15478076 pairs aligned 0 times concordantly or discordantly; of these: 30956152 mates make up the pairs; of these: 29134568 (94.12%) aligned 0 times 1047226 (3.38%) aligned exactly 1 time 774358 (2.50%) aligned >1 times 25.97% overall alignment rate Time searching: 00:23:40 Overall time: 00:23:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 3334110 / 4135003 = 0.8063 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:12:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 06:12:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:12:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:12:17: 1000000 INFO @ Sat, 11 Dec 2021 06:12:25: 2000000 INFO @ Sat, 11 Dec 2021 06:12:33: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:12:38: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:12:38: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:12:38: #1 total tags in treatment: 669622 INFO @ Sat, 11 Dec 2021 06:12:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:12:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:12:38: #1 tags after filtering in treatment: 528195 INFO @ Sat, 11 Dec 2021 06:12:38: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 06:12:38: #1 finished! INFO @ Sat, 11 Dec 2021 06:12:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:12:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:12:38: #2 number of paired peaks: 2885 INFO @ Sat, 11 Dec 2021 06:12:38: start model_add_line... INFO @ Sat, 11 Dec 2021 06:12:38: start X-correlation... INFO @ Sat, 11 Dec 2021 06:12:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 06:12:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:12:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:12:38: end of X-cor INFO @ Sat, 11 Dec 2021 06:12:38: #2 finished! INFO @ Sat, 11 Dec 2021 06:12:38: #2 predicted fragment length is 173 bps INFO @ Sat, 11 Dec 2021 06:12:38: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 11 Dec 2021 06:12:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.05_model.r WARNING @ Sat, 11 Dec 2021 06:12:38: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:12:38: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Sat, 11 Dec 2021 06:12:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:12:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:12:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:12:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:12:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:12:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.05_summits.bed INFO @ Sat, 11 Dec 2021 06:12:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1924 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:12:46: 1000000 INFO @ Sat, 11 Dec 2021 06:12:54: 2000000 INFO @ Sat, 11 Dec 2021 06:13:03: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:13:07: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:13:07: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:13:07: #1 total tags in treatment: 669622 INFO @ Sat, 11 Dec 2021 06:13:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:13:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:13:07: #1 tags after filtering in treatment: 528195 INFO @ Sat, 11 Dec 2021 06:13:07: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 06:13:07: #1 finished! INFO @ Sat, 11 Dec 2021 06:13:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:13:07: #2 number of paired peaks: 2885 INFO @ Sat, 11 Dec 2021 06:13:07: start model_add_line... INFO @ Sat, 11 Dec 2021 06:13:07: start X-correlation... INFO @ Sat, 11 Dec 2021 06:13:07: end of X-cor INFO @ Sat, 11 Dec 2021 06:13:07: #2 finished! INFO @ Sat, 11 Dec 2021 06:13:07: #2 predicted fragment length is 173 bps INFO @ Sat, 11 Dec 2021 06:13:07: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 11 Dec 2021 06:13:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.10_model.r WARNING @ Sat, 11 Dec 2021 06:13:07: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:13:07: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Sat, 11 Dec 2021 06:13:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:13:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:13:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:13:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 06:13:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:13:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:13:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:13:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:13:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:13:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.10_summits.bed INFO @ Sat, 11 Dec 2021 06:13:09: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1138 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:13:16: 1000000 INFO @ Sat, 11 Dec 2021 06:13:24: 2000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:13:34: 3000000 INFO @ Sat, 11 Dec 2021 06:13:38: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:13:38: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:13:38: #1 total tags in treatment: 669622 INFO @ Sat, 11 Dec 2021 06:13:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:13:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:13:38: #1 tags after filtering in treatment: 528195 INFO @ Sat, 11 Dec 2021 06:13:38: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 06:13:38: #1 finished! INFO @ Sat, 11 Dec 2021 06:13:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:13:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:13:38: #2 number of paired peaks: 2885 INFO @ Sat, 11 Dec 2021 06:13:38: start model_add_line... INFO @ Sat, 11 Dec 2021 06:13:38: start X-correlation... INFO @ Sat, 11 Dec 2021 06:13:38: end of X-cor INFO @ Sat, 11 Dec 2021 06:13:38: #2 finished! INFO @ Sat, 11 Dec 2021 06:13:38: #2 predicted fragment length is 173 bps INFO @ Sat, 11 Dec 2021 06:13:38: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 11 Dec 2021 06:13:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.20_model.r WARNING @ Sat, 11 Dec 2021 06:13:38: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:13:38: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Sat, 11 Dec 2021 06:13:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:13:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:13:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:13:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:13:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:13:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:13:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556381/SRX8556381.20_summits.bed INFO @ Sat, 11 Dec 2021 06:13:40: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (560 records, 4 fields): 2 millis CompletedMACS2peakCalling